Just curious, what are you trying to end up with? Do you want the scope to end up optically centered when it is zeroed at 100 yds, or how many moa of elevation do you wanna end up with?

Reason I ask is I dont know why the scope rep would assure you a 20moa base would not help you gain some adjustment.

Couple other things to check:
- Are you sure the front of the base isnt sitting on the recoil lug and making it higher in the front? That would cause what you are saying.
- Maybe take the scope off and put another scope in the same ring/base combo and see if it has the same problem, just to rule out a problem with the scopes adjustments. Just because the parts are expensive and made by NF dont mean they cant be defective. May not be the problem, but it is an easy way to rule it out.